Manuscripts

SELECTED MANUSCRIPTS

Ghiotto G., Xirostylidou A., Gaspari M., Kougias P.G., Campanaro S., Treu L. Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics. Cell Genom. 2025 Sep 10;5(9):100949. 10.1016/j.xgen.2025.100949

D. Sanguineti, A. Chatzis, G. Zampieri, M. Gaspari, P.G. Kougias, Campanaro S., Treu L. Modelling microbial and metabolic shifts in trickle bed reactor biomethanation at decreasing gas retention times. Chemical Engineering Journal, 167574 10.1016/j.cej.2025.167574

Orellana E., Zampieri G., De Bernardini N., Guerrero L.D., Erijman L., Campanaro S., Treu L. Sustainable Food Waste Management in Anaerobic Digesters: prediction of organic load impact by Metagenome-Scale Metabolic Modeling. 2025 Environmental Science & Technology. 10.1021/acs.est.4c11180

Santinello D., Zampieri G., Agostini S., Müller B., Favaro L., Treu L., Campanaro S. Process stability in Anaerobic Digestion: unveiling microbial signatures of full-scale reactor performance. 2024 Chemical Engineering Journal. 10.1016/j.biortech.2022.127701  

Zampieri, G., Santinello, D., Palù, M., Orellana, E., Costantini, P., Favaro, L., Campanaro, S., & Treu, L. (2025). Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota. The ISME Journal, wraf017. 10.1093/ismejo/wraf017

Ghiotto G., De Bernardini N., Orellana E., Fiorito G., Cenci L., Kougias P.G., Campanaro S., Treu L. Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation. 2025 npj Biofilms Microbiomes (IF 7.8) 10.1038/s41522-025-00649-2 

De Bernardini N., Zampieri G., Campanaro S., Zimmermann J., Waschina S., Treu L. pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes. 2024 Genome Biology (IF 10.1) 10.1186/s13059-024-03425-1

Ghiotto G., Detman-Ignatowska A., Chojnacka A., Orellana E., de Bernardini N., Fraulini S., Treu L., Sikora A., Campanaro S. Decipher syntrophies within C2-C4 organic acids-degrading anaerobic microbiomes: a multi-omic exploration. 2024 Chemical Engineering Journal (IF 15.1) 10.1016/j.cej.2024.151390

Serna-García R., Morlino M.S., Bucci L., Savio F., Favaro L., Morosinotto T., Seco A., Bouzas A., Campanaro S., Treu L. Biological carbon capture from biogas streams: insights into Cupriavidus necator autotrophic growth and transcriptional profile. 2024 Bioresource Technology (IF 11.4) 10.1016/j.biortech.2024.130556

Agostini S., Bucci L., Doni D., Costantini P., Gupte A., Müller B., Sibilla F., Basaglia M., Casella S., Favaro L., Campanaro S., Treu L. Bioaugmentation strategies based on bacterial and methanogenic cultures to relieve stress in anaerobic digestion of protein-rich substrates. 2024 Renewable Energy (IF 8.7) 10.1016/j.renene.2024.120270

Ghiotto G., De Bernardini N., Giangeri G., Tsapekos P., Gaspari M., Kougias P.G., Campanaro S., Angelidaki I., Treu L. From Microbial Heterogeneity to Evolutionary Insights: A Strain-Resolved Metagenomic Study of H2S-Induced Changes in Anaerobic Biofilms. 2024 Chemical Engineering Journal (IF 15.1) 10.1016/j.cej.2024.149824

Ghiotto G., Zampieri G., Campanaro S., Treu L. Strain-resolved metagenomics approaches applied to biogas upgrading. 2024 Environmental Research (IF 8.3) 10.1016/j.envres.2023.117414

Bucci L., Ghiotto G., Zampieri G., Raga R., Favaro L., Treu L., Campanaro S. Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics. 2023 Environmental Science & Technology (IF 11.4) 10.1021/acs.est.3c07737

Morlino M.S., Serna García R., Savio F., Zampieri G., Morosinotto T., Treu L., Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. 2023 Biotechnology Advances (IF 16.0) 10.1016/j.biotechadv.2023.108264

Basile A., Zampieri G., Kovalovszki A., Karkaria B., Treu L., Patil K.R., Campanaro S. Modelling of microbial interactions in anaerobic digestion: from black to glass box. 2023 Current Opinion in Microbiology (IF 5.4) 10.1016/j.mib.2023.102363

Ji M., Giangeri G., Usman M., Liu L., Bosaro M., Sessa F., Canu P., Treu L., Campanaro S. An Integrated Metagenomic-Pangenomic Strategy Revealed Native Microbes and Magnetic Biochar Cooperation in Plasticizer Degradation. 2023 Chemical Engineering Journal (IF 15.1) 10.1016/j.cej.2023.143589

Zampieri G., Angione C., Palù M., Campanaro S., Treu L. Metatranscriptomics-guided genome-scale metabolic modelling of microbial communities. 2023 Cell Reports Methods (IF 3.8) 10.1016/j.crmeth.2022.100383

Basile A., Heinken A., Hertel J., Smarr L., Li W., Treu L., Valle G., Campanaro S.*, Thiele I.* Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. 2023 Gut Microbes (IF 12.2) 10.1080/19490976.2023.2226921

Ji M., Giangeri G., Fengbo Y., Sessa F., Liu C., Wenjing S., Canu P., Fangbai L., Treu L., Campanaro S. An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil. 2023 Journal of Hazardous Materials (IF 13.6) 10.1016/j.jhazmat.2023.131950

Rossi A., Morlino M.S., Gaspari M., Basile A., Kougias P.G., Treu L., Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. 2022 Microbiome (IF 15.5) 10.1186/s40168-022-01316-w

De Bernardini N., Basile A., Zampieri G., Kovalovszki A., De Diego Diaz B., Offer E., Wongfaed N., Angelidaki I., Kougias P.G., Campanaro S., Treu L. Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation. 2022 Microbiome (IF 15.5) 

Giangeri G., Morlino M.S., De Bernardini N., Ji M., Bosaro M., Pirillo V., Antoniali P., Molla G., Raga R., Treu L., Campanaro S. Preliminary investigation of microorganisms potentially involved in microplastics degradation using an integrated metagenomics and biochemical approach. 2022 Science of the Total Environment (IF 9.8) 

Palù M., Basile A., Zampieri G., Treu L., Rossi A., Morlino M.S., Campanaro S. KEMET – A python tool for KEGG Module evaluation and microbial genome annotation expansion. 2022 Computational and Structural Biotechnology Journal (IF 6.0) 10.1016/j.csbj.2022.03.015

Palù M., Peprah M., Tsapekos P., Kougias P.G., Campanaro S., Angelidaki I., Treu L. In-situ biogas upgrading assisted by bioaugmentation with hydrogenotrophic methanogens during mesophilic and thermophilic co-digestion. 2022 Bioresource Technology (IF 11.4) 10.1016/j.biortech.2022.126754

Basile A., De Pascale F., Bianca F., Rossi A., Frizzarin M., De Bernardini N., Bosaro M., Baldisseri A., Antoniali P., Lopreiato R., Treu L., Campanaro S. Large-scale sequencing and comparative analysis of oenological Saccharomyces cerevisiae strains supported by nanopore refinement of key genomes. 2021 Food Microbiology (IF 6.4) 10.1016/j.fm.2021.103753

Basile A., Campanaro S., Kovalovszki A., Zampieri G., Rossi A., Angelidaki I., Valle G., Treu L. Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis. 2020 Metabolic Engineering (IF 9.0) 10.1016/j.ymben.2020.08.013

Rossi A., Treu L., Toppo S., Zschach H., Campanaro S., Dutilh B.E. Evolutionary study of the crAssphage virus at gene level. 2020 Viruses (IF 5.0) 10.3390/v12091035

Campanaro, S., Treu, L., Rodriguez-R, L., Kovalovszki, A., Ziels, R., Maus, I., Zhu, X., Kougias, P.G., Basile, A., Luo, G., Schluter, A., Konstantinidis, K., Angelidaki, I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. 2020 Biotechnology for Biofuels (IF 6.0) 10.1186/s13068-020-01679-y

Zhu, X., Campanaro, S., Treu, L., Kougias, P.G., Kyrpides N., Angelidaki, I. Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem. 2020 Microbiome (IF 14.7) 10.1186/s40168-019-0780-9

Treu, L., Kougias, P.G., Campanaro, S., de Diego-Diaz, B., Bassani, I., Angelidaki, I. Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration. 2018 Bioresource Technology (IF 6.7) 10.1016/j.biortech.2018.05.070

Campanaro, S., Treu, L., Luo, G., Kougias, P.G., Angelidaki, I. Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants. 2018 Water Research (IF 7.9) 10.1016/j.watres.2018.04.043

Treu, L., Campanaro, S., Kougias, P.G., Zhu, X. and Angelidaki, I. Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members. 2016 Environmental Science & Technology (IF 6.2) 10.1021/acs.est.6b00296

Campanaro, S., Treu, L., Kougias, P.G., De Francisci, D., Valle, G. and Angelidaki, I. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. 2016 Biotechnology for Biofuels (IF 5.2) 10.1186/s13068-016-0441-1

Treu, L., Toniolo, C., Nadai, C., Sardu, A., Giacomini, A., Corich, V., Campanaro, S. The impact of genomic variability on gene expression in environmental Saccharomyces cerevisiae strains. 2014 Environmental Microbiology (IF 6.2) 10.1111/1462-2920.12327

Campanaro, S., Williams, T.J., Burg, D.W., De Francisci, D., Treu, L., Lauro, F.M., Cavicchioli, R. Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii 2011 Environmental Microbiology, (IF 5.5) 10.1111/j.1462-2920.2010.02367.x

Vezzi, A., Campanaro, S., D'Angelo, M., Simonato, F., Vitulo, N., Lauro, F.M., Cestaro, A., Malacrida, G., Simionati, B., Cannata, N., Romualdi, C., Bartlett, D.H., Valle, G. Life at depth: Photobacterium profundum genome sequence and expression analysis 2005 Science (IF 31.9) 10.1126/science.1103341

Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., Arkin, A.P., Astromoff, A., El Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S. … Johnston, M. Functional profiling of the Saccharomyces cerevisiae genome 2002 Nature (IF 30.4) 10.1038/nature00935